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root/OpenMD/branches/development/src/rnemd/RNEMD.cpp

Comparing branches/development/src/rnemd/RNEMD.cpp (file contents):
Revision 1773 by gezelter, Tue Aug 7 18:26:40 2012 UTC vs.
Revision 1867 by gezelter, Mon Apr 29 17:53:48 2013 UTC

#	Line 35 | Line 35
35		*
36		* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37		* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	<	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
38	>	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39		* [4]  Vardeman & Gezelter, in progress (2009).
40		*/
41
42		#include <cmath>
43	+	#include <sstream>
44	+	#include <string>
45	+
46		#include "rnemd/RNEMD.hpp"
47		#include "math/Vector3.hpp"
48		#include "math/Vector.hpp"
#	Line 49 | Line 52
52		#include "primitives/StuntDouble.hpp"
53		#include "utils/PhysicalConstants.hpp"
54		#include "utils/Tuple.hpp"
55	+	#include "brains/Thermo.hpp"
56	+	#include "math/ConvexHull.hpp"
57		#ifdef IS_MPI
58		#include <mpi.h>
59		#endif
60
61	+	#ifdef _MSC_VER
62	+	#define isnan(x) _isnan((x))
63	+	#define isinf(x) (!_finite(x) && !_isnan(x))
64	+	#endif
65	+
66		#define HONKING_LARGE_VALUE 1.0e10
67
68		using namespace std;
69		namespace OpenMD {
70
71		RNEMD::RNEMD(SimInfo* info) : info_(info), evaluator_(info), seleMan_(info),
72	+	evaluatorA_(info), seleManA_(info),
73	+	commonA_(info), evaluatorB_(info),
74	+	seleManB_(info), commonB_(info),
75		usePeriodicBoundaryConditions_(info->getSimParams()->getUsePeriodicBoundaryConditions()) {
76
77		trialCount_ = 0;
78		failTrialCount_ = 0;
79		failRootCount_ = 0;
80
81	<	int seedValue;
69	<	Globals * simParams = info->getSimParams();
81	>	Globals* simParams = info->getSimParams();
82		RNEMDParameters* rnemdParams = simParams->getRNEMDParameters();
83
84	+	doRNEMD_ = rnemdParams->getUseRNEMD();
85	+	if (!doRNEMD_) return;
86	+
87		stringToMethod_["Swap"]  = rnemdSwap;
88		stringToMethod_["NIVS"]  = rnemdNIVS;
89		stringToMethod_["VSS"]   = rnemdVSS;
#	Line 77 | Line 92 | namespace OpenMD {
92		stringToFluxType_["Px"]  = rnemdPx;
93		stringToFluxType_["Py"]  = rnemdPy;
94		stringToFluxType_["Pz"]  = rnemdPz;
95	+	stringToFluxType_["Pvector"]  = rnemdPvector;
96	+	stringToFluxType_["Lx"]  = rnemdLx;
97	+	stringToFluxType_["Ly"]  = rnemdLy;
98	+	stringToFluxType_["Lz"]  = rnemdLz;
99	+	stringToFluxType_["Lvector"]  = rnemdLvector;
100		stringToFluxType_["KE+Px"]  = rnemdKePx;
101		stringToFluxType_["KE+Py"]  = rnemdKePy;
102		stringToFluxType_["KE+Pvector"]  = rnemdKePvector;
103	+	stringToFluxType_["KE+Lx"]  = rnemdKeLx;
104	+	stringToFluxType_["KE+Ly"]  = rnemdKeLy;
105	+	stringToFluxType_["KE+Lz"]  = rnemdKeLz;
106	+	stringToFluxType_["KE+Lvector"]  = rnemdKeLvector;
107
108		runTime_ = simParams->getRunTime();
109		statusTime_ = simParams->getStatusTime();
110
87	–	rnemdObjectSelection_ = rnemdParams->getObjectSelection();
88	–	evaluator_.loadScriptString(rnemdObjectSelection_);
89	–	seleMan_.setSelectionSet(evaluator_.evaluate());
90	–
111		const string methStr = rnemdParams->getMethod();
112		bool hasFluxType = rnemdParams->haveFluxType();
113
114	+	rnemdObjectSelection_ = rnemdParams->getObjectSelection();
115	+
116		string fluxStr;
117		if (hasFluxType) {
118		fluxStr = rnemdParams->getFluxType();
#	Line 98 | Line 120 | namespace OpenMD {
120		sprintf(painCave.errMsg,
121		"RNEMD: No fluxType was set in the md file.  This parameter,\n"
122		"\twhich must be one of the following values:\n"
123	<	"\tKE, Px, Py, Pz, KE+Px, KE+Py, KE+Pvector, must be set to\n"
124	<	"\tuse RNEMD\n");
123	>	"\tKE, Px, Py, Pz, Pvector, Lx, Ly, Lz, Lvector,\n"
124	>	"\tKE+Px, KE+Py, KE+Pvector, KE+Lx, KE+Ly, KE+Lz, KE+Lvector\n"
125	>	"\tmust be set to use RNEMD\n");
126		painCave.isFatal = 1;
127		painCave.severity = OPENMD_ERROR;
128		simError();
#	Line 108 | Line 131 | namespace OpenMD {
131		bool hasKineticFlux = rnemdParams->haveKineticFlux();
132		bool hasMomentumFlux = rnemdParams->haveMomentumFlux();
133		bool hasMomentumFluxVector = rnemdParams->haveMomentumFluxVector();
134	+	bool hasAngularMomentumFlux = rnemdParams->haveAngularMomentumFlux();
135	+	bool hasAngularMomentumFluxVector = rnemdParams->haveAngularMomentumFluxVector();
136	+	hasSelectionA_ = rnemdParams->haveSelectionA();
137	+	hasSelectionB_ = rnemdParams->haveSelectionB();
138		bool hasSlabWidth = rnemdParams->haveSlabWidth();
139		bool hasSlabACenter = rnemdParams->haveSlabACenter();
140		bool hasSlabBCenter = rnemdParams->haveSlabBCenter();
141	+	bool hasSphereARadius = rnemdParams->haveSphereARadius();
142	+	hasSphereBRadius_ = rnemdParams->haveSphereBRadius();
143	+	bool hasCoordinateOrigin = rnemdParams->haveCoordinateOrigin();
144		bool hasOutputFileName = rnemdParams->haveOutputFileName();
145		bool hasOutputFields = rnemdParams->haveOutputFields();
146
#	Line 195 | Line 225 | namespace OpenMD {
225		case rnemdPz:
226		hasCorrectFlux = hasMomentumFlux;
227		break;
228	+	case rnemdLx:
229	+	case rnemdLy:
230	+	case rnemdLz:
231	+	hasCorrectFlux = hasAngularMomentumFlux;
232	+	break;
233		case rnemdPvector:
234		hasCorrectFlux = hasMomentumFluxVector;
235	+	break;
236	+	case rnemdLvector:
237	+	hasCorrectFlux = hasAngularMomentumFluxVector;
238	+	break;
239		case rnemdKePx:
240		case rnemdKePy:
241		hasCorrectFlux = hasMomentumFlux && hasKineticFlux;
242		break;
243	+	case rnemdKeLx:
244	+	case rnemdKeLy:
245	+	case rnemdKeLz:
246	+	hasCorrectFlux = hasAngularMomentumFlux && hasKineticFlux;
247	+	break;
248		case rnemdKePvector:
249		hasCorrectFlux = hasMomentumFluxVector && hasKineticFlux;
250		break;
251	+	case rnemdKeLvector:
252	+	hasCorrectFlux = hasAngularMomentumFluxVector && hasKineticFlux;
253	+	break;
254		default:
255		methodFluxMismatch = true;
256		break;
#	Line 224 | Line 271 | namespace OpenMD {
271		}
272		if (!hasCorrectFlux) {
273		sprintf(painCave.errMsg,
274	<	"RNEMD: The current method,\n"
228	<	"\t%s, and flux type %s\n"
274	>	"RNEMD: The current method, %s, and flux type, %s,\n"
275		"\tdid not have the correct flux value specified. Options\n"
276	<	"\tinclude: kineticFlux, momentumFlux, and momentumFluxVector\n",
276	>	"\tinclude: kineticFlux, momentumFlux, angularMomentumFlux,\n"
277	>	"\tmomentumFluxVector, and angularMomentumFluxVector.\n",
278		methStr.c_str(), fluxStr.c_str());
279		painCave.isFatal = 1;
280		painCave.severity = OPENMD_ERROR;
#	Line 235 | Line 282 | namespace OpenMD {
282		}
283
284		if (hasKineticFlux) {
285	<	kineticFlux_ = rnemdParams->getKineticFlux();
285	>	// convert the kcal / mol / Angstroms^2 / fs values in the md file
286	>	// into  amu / fs^3:
287	>	kineticFlux_ = rnemdParams->getKineticFlux()
288	>	* PhysicalConstants::energyConvert;
289		} else {
290		kineticFlux_ = 0.0;
291		}
#	Line 264 | Line 314 | namespace OpenMD {
314		default:
315		break;
316		}
317	<	}
318	<	}
319	<
320	<	// do some sanity checking
321	<
322	<	int selectionCount = seleMan_.getSelectionCount();
323	<	int nIntegrable = info->getNGlobalIntegrableObjects();
324	<
325	<	if (selectionCount > nIntegrable) {
326	<	sprintf(painCave.errMsg,
327	<	"RNEMD: The current objectSelection,\n"
328	<	"\t\t%s\n"
329	<	"\thas resulted in %d selected objects.  However,\n"
330	<	"\tthe total number of integrable objects in the system\n"
331	<	"\tis only %d.  This is almost certainly not what you want\n"
332	<	"\tto do.  A likely cause of this is forgetting the _RB_0\n"
333	<	"\tselector in the selection script!\n",
334	<	rnemdObjectSelection_.c_str(),
335	<	selectionCount, nIntegrable);
336	<	painCave.isFatal = 0;
337	<	painCave.severity = OPENMD_WARNING;
338	<	simError();
339	<	}
340	<
341	<	nBins_ = rnemdParams->getOutputBins();
317	>	}
318	>	if (hasAngularMomentumFluxVector) {
319	>	angularMomentumFluxVector_ = rnemdParams->getAngularMomentumFluxVector();
320	>	} else {
321	>	angularMomentumFluxVector_ = V3Zero;
322	>	if (hasAngularMomentumFlux) {
323	>	RealType angularMomentumFlux = rnemdParams->getAngularMomentumFlux();
324	>	switch (rnemdFluxType_) {
325	>	case rnemdLx:
326	>	angularMomentumFluxVector_.x() = angularMomentumFlux;
327	>	break;
328	>	case rnemdLy:
329	>	angularMomentumFluxVector_.y() = angularMomentumFlux;
330	>	break;
331	>	case rnemdLz:
332	>	angularMomentumFluxVector_.z() = angularMomentumFlux;
333	>	break;
334	>	case rnemdKeLx:
335	>	angularMomentumFluxVector_.x() = angularMomentumFlux;
336	>	break;
337	>	case rnemdKeLy:
338	>	angularMomentumFluxVector_.y() = angularMomentumFlux;
339	>	break;
340	>	case rnemdKeLz:
341	>	angularMomentumFluxVector_.z() = angularMomentumFlux;
342	>	break;
343	>	default:
344	>	break;
345	>	}
346	>	}
347	>	}
348
349	<	data_.resize(RNEMD::ENDINDEX);
350	<	OutputData z;
351	<	z.units =  "Angstroms";
352	<	z.title =  "Z";
353	<	z.dataType = "RealType";
298	<	z.accumulator.reserve(nBins_);
299	<	for (unsigned int i = 0; i < nBins_; i++)
300	<	z.accumulator.push_back( new Accumulator() );
301	<	data_[Z] = z;
302	<	outputMap_["Z"] =  Z;
349	>	if (hasCoordinateOrigin) {
350	>	coordinateOrigin_ = rnemdParams->getCoordinateOrigin();
351	>	} else {
352	>	coordinateOrigin_ = V3Zero;
353	>	}
354
355	<	OutputData temperature;
305	<	temperature.units =  "K";
306	<	temperature.title =  "Temperature";
307	<	temperature.dataType = "RealType";
308	<	temperature.accumulator.reserve(nBins_);
309	<	for (unsigned int i = 0; i < nBins_; i++)
310	<	temperature.accumulator.push_back( new Accumulator() );
311	<	data_[TEMPERATURE] = temperature;
312	<	outputMap_["TEMPERATURE"] =  TEMPERATURE;
355	>	// do some sanity checking
356
357	<	OutputData velocity;
315	<	velocity.units = "amu/fs";
316	<	velocity.title =  "Velocity";
317	<	velocity.dataType = "Vector3d";
318	<	velocity.accumulator.reserve(nBins_);
319	<	for (unsigned int i = 0; i < nBins_; i++)
320	<	velocity.accumulator.push_back( new VectorAccumulator() );
321	<	data_[VELOCITY] = velocity;
322	<	outputMap_["VELOCITY"] = VELOCITY;
357	>	int selectionCount = seleMan_.getSelectionCount();
358
359	<	OutputData density;
325	<	density.units =  "g cm^-3";
326	<	density.title =  "Density";
327	<	density.dataType = "RealType";
328	<	density.accumulator.reserve(nBins_);
329	<	for (unsigned int i = 0; i < nBins_; i++)
330	<	density.accumulator.push_back( new Accumulator() );
331	<	data_[DENSITY] = density;
332	<	outputMap_["DENSITY"] =  DENSITY;
359	>	int nIntegrable = info->getNGlobalIntegrableObjects();
360
361	<	if (hasOutputFields) {
362	<	parseOutputFileFormat(rnemdParams->getOutputFields());
363	<	} else {
364	<	outputMask_.set(Z);
365	<	switch (rnemdFluxType_) {
366	<	case rnemdKE:
367	<	case rnemdRotKE:
368	<	case rnemdFullKE:
369	<	outputMask_.set(TEMPERATURE);
370	<	break;
371	<	case rnemdPx:
372	<	case rnemdPy:
373	<	outputMask_.set(VELOCITY);
374	<	break;
375	<	case rnemdPz:
376	<	case rnemdPvector:
377	<	outputMask_.set(VELOCITY);
378	<	outputMask_.set(DENSITY);
379	<	break;
380	<	case rnemdKePx:
381	<	case rnemdKePy:
382	<	outputMask_.set(TEMPERATURE);
383	<	outputMask_.set(VELOCITY);
384	<	break;
385	<	case rnemdKePvector:
386	<	outputMask_.set(TEMPERATURE);
387	<	outputMask_.set(VELOCITY);
388	<	outputMask_.set(DENSITY);
389	<	break;
390	<	default:
391	<	break;
392	<	}
393	<	}
394	<
395	<	if (hasOutputFileName) {
396	<	rnemdFileName_ = rnemdParams->getOutputFileName();
397	<	} else {
398	<	rnemdFileName_ = getPrefix(info->getFinalConfigFileName()) + ".rnemd";
399	<	}
361	>	if (selectionCount > nIntegrable) {
362	>	sprintf(painCave.errMsg,
363	>	"RNEMD: The current objectSelection,\n"
364	>	"\t\t%s\n"
365	>	"\thas resulted in %d selected objects.  However,\n"
366	>	"\tthe total number of integrable objects in the system\n"
367	>	"\tis only %d.  This is almost certainly not what you want\n"
368	>	"\tto do.  A likely cause of this is forgetting the _RB_0\n"
369	>	"\tselector in the selection script!\n",
370	>	rnemdObjectSelection_.c_str(),
371	>	selectionCount, nIntegrable);
372	>	painCave.isFatal = 0;
373	>	painCave.severity = OPENMD_WARNING;
374	>	simError();
375	>	}
376	>
377	>	areaAccumulator_ = new Accumulator();
378	>
379	>	nBins_ = rnemdParams->getOutputBins();
380	>	binWidth_ = rnemdParams->getOutputBinWidth();
381	>
382	>	data_.resize(RNEMD::ENDINDEX);
383	>	OutputData z;
384	>	z.units =  "Angstroms";
385	>	z.title =  "Z";
386	>	z.dataType = "RealType";
387	>	z.accumulator.reserve(nBins_);
388	>	for (int i = 0; i < nBins_; i++)
389	>	z.accumulator.push_back( new Accumulator() );
390	>	data_[Z] = z;
391	>	outputMap_["Z"] =  Z;
392	>
393	>	OutputData r;
394	>	r.units =  "Angstroms";
395	>	r.title =  "R";
396	>	r.dataType = "RealType";
397	>	r.accumulator.reserve(nBins_);
398	>	for (int i = 0; i < nBins_; i++)
399	>	r.accumulator.push_back( new Accumulator() );
400	>	data_[R] = r;
401	>	outputMap_["R"] =  R;
402
403	<	exchangeTime_ = rnemdParams->getExchangeTime();
403	>	OutputData temperature;
404	>	temperature.units =  "K";
405	>	temperature.title =  "Temperature";
406	>	temperature.dataType = "RealType";
407	>	temperature.accumulator.reserve(nBins_);
408	>	for (int i = 0; i < nBins_; i++)
409	>	temperature.accumulator.push_back( new Accumulator() );
410	>	data_[TEMPERATURE] = temperature;
411	>	outputMap_["TEMPERATURE"] =  TEMPERATURE;
412
413	<	Snapshot* currentSnap_ = info->getSnapshotManager()->getCurrentSnapshot();
414	<	Mat3x3d hmat = currentSnap_->getHmat();
415	<
416	<	// Target exchange quantities (in each exchange) =  2 Lx Ly dt flux
417	<	// Lx, Ly = box dimensions in x & y
418	<	// dt = exchange time interval
419	<	// flux = target flux
413	>	OutputData velocity;
414	>	velocity.units = "angstroms/fs";
415	>	velocity.title =  "Velocity";
416	>	velocity.dataType = "Vector3d";
417	>	velocity.accumulator.reserve(nBins_);
418	>	for (int i = 0; i < nBins_; i++)
419	>	velocity.accumulator.push_back( new VectorAccumulator() );
420	>	data_[VELOCITY] = velocity;
421	>	outputMap_["VELOCITY"] = VELOCITY;
422
423	<	kineticTarget_ = 2.0*kineticFlux_*exchangeTime_*hmat(0,0)*hmat(1,1);
424	<	momentumTarget_ = 2.0*momentumFluxVector_*exchangeTime_*hmat(0,0)*hmat(1,1);
423	>	OutputData angularVelocity;
424	>	angularVelocity.units = "angstroms^2/fs";
425	>	angularVelocity.title =  "AngularVelocity";
426	>	angularVelocity.dataType = "Vector3d";
427	>	angularVelocity.accumulator.reserve(nBins_);
428	>	for (int i = 0; i < nBins_; i++)
429	>	angularVelocity.accumulator.push_back( new VectorAccumulator() );
430	>	data_[ANGULARVELOCITY] = angularVelocity;
431	>	outputMap_["ANGULARVELOCITY"] = ANGULARVELOCITY;
432
433	<	// total exchange sums are zeroed out at the beginning:
433	>	OutputData density;
434	>	density.units =  "g cm^-3";
435	>	density.title =  "Density";
436	>	density.dataType = "RealType";
437	>	density.accumulator.reserve(nBins_);
438	>	for (int i = 0; i < nBins_; i++)
439	>	density.accumulator.push_back( new Accumulator() );
440	>	data_[DENSITY] = density;
441	>	outputMap_["DENSITY"] =  DENSITY;
442
443	<	kineticExchange_ = 0.0;
444	<	momentumExchange_ = V3Zero;
443	>	if (hasOutputFields) {
444	>	parseOutputFileFormat(rnemdParams->getOutputFields());
445	>	} else {
446	>	if (usePeriodicBoundaryConditions_)
447	>	outputMask_.set(Z);
448	>	else
449	>	outputMask_.set(R);
450	>	switch (rnemdFluxType_) {
451	>	case rnemdKE:
452	>	case rnemdRotKE:
453	>	case rnemdFullKE:
454	>	outputMask_.set(TEMPERATURE);
455	>	break;
456	>	case rnemdPx:
457	>	case rnemdPy:
458	>	outputMask_.set(VELOCITY);
459	>	break;
460	>	case rnemdPz:
461	>	case rnemdPvector:
462	>	outputMask_.set(VELOCITY);
463	>	outputMask_.set(DENSITY);
464	>	break;
465	>	case rnemdLx:
466	>	case rnemdLy:
467	>	case rnemdLz:
468	>	case rnemdLvector:
469	>	outputMask_.set(ANGULARVELOCITY);
470	>	break;
471	>	case rnemdKeLx:
472	>	case rnemdKeLy:
473	>	case rnemdKeLz:
474	>	case rnemdKeLvector:
475	>	outputMask_.set(TEMPERATURE);
476	>	outputMask_.set(ANGULARVELOCITY);
477	>	break;
478	>	case rnemdKePx:
479	>	case rnemdKePy:
480	>	outputMask_.set(TEMPERATURE);
481	>	outputMask_.set(VELOCITY);
482	>	break;
483	>	case rnemdKePvector:
484	>	outputMask_.set(TEMPERATURE);
485	>	outputMask_.set(VELOCITY);
486	>	outputMask_.set(DENSITY);
487	>	break;
488	>	default:
489	>	break;
490	>	}
491	>	}
492	>
493	>	if (hasOutputFileName) {
494	>	rnemdFileName_ = rnemdParams->getOutputFileName();
495	>	} else {
496	>	rnemdFileName_ = getPrefix(info->getFinalConfigFileName()) + ".rnemd";
497	>	}
498
499	<	if (hasSlabWidth)
500	<	slabWidth_ = rnemdParams->getSlabWidth();
501	<	else
502	<	slabWidth_ = hmat(2,2) / 10.0;
503	<
504	<	if (hasSlabACenter)
505	<	slabACenter_ = rnemdParams->getSlabACenter();
506	<	else
507	<	slabACenter_ = 0.0;
499	>	exchangeTime_ = rnemdParams->getExchangeTime();
500	>
501	>	Snapshot* currentSnap_ = info->getSnapshotManager()->getCurrentSnapshot();
502	>	// total exchange sums are zeroed out at the beginning:
503	>
504	>	kineticExchange_ = 0.0;
505	>	momentumExchange_ = V3Zero;
506	>	angularMomentumExchange_ = V3Zero;
507	>
508	>	std::ostringstream selectionAstream;
509	>	std::ostringstream selectionBstream;
510
511	<	if (hasSlabBCenter)
512	<	slabBCenter_ = rnemdParams->getSlabBCenter();
513	<	else
514	<	slabBCenter_ = hmat(2,2) / 2.0;
511	>	if (hasSelectionA_) {
512	>	selectionA_ = rnemdParams->getSelectionA();
513	>	} else {
514	>	if (usePeriodicBoundaryConditions_) {
515	>	Mat3x3d hmat = currentSnap_->getHmat();
516	>
517	>	if (hasSlabWidth)
518	>	slabWidth_ = rnemdParams->getSlabWidth();
519	>	else
520	>	slabWidth_ = hmat(2,2) / 10.0;
521	>
522	>	if (hasSlabACenter)
523	>	slabACenter_ = rnemdParams->getSlabACenter();
524	>	else
525	>	slabACenter_ = 0.0;
526	>
527	>	selectionAstream << "select wrappedz > "
528	>	<< slabACenter_ - 0.5*slabWidth_
529	>	<<  " && wrappedz < "
530	>	<< slabACenter_ + 0.5*slabWidth_;
531	>	selectionA_ = selectionAstream.str();
532	>	} else {
533	>	if (hasSphereARadius)
534	>	sphereARadius_ = rnemdParams->getSphereARadius();
535	>	else {
536	>	// use an initial guess to the size of the inner slab to be 1/10 the
537	>	// radius of an approximately spherical hull:
538	>	Thermo thermo(info);
539	>	RealType hVol = thermo.getHullVolume();
540	>	sphereARadius_ = 0.1 * pow((3.0 * hVol / (4.0 * M_PI)), 1.0/3.0);
541	>	}
542	>	selectionAstream << "select r < " << sphereARadius_;
543	>	selectionA_ = selectionAstream.str();
544	>	}
545	>	}
546
547	+	if (hasSelectionB_) {
548	+	selectionB_ = rnemdParams->getSelectionB();
549	+	} else {
550	+	if (usePeriodicBoundaryConditions_) {
551	+	Mat3x3d hmat = currentSnap_->getHmat();
552	+
553	+	if (hasSlabWidth)
554	+	slabWidth_ = rnemdParams->getSlabWidth();
555	+	else
556	+	slabWidth_ = hmat(2,2) / 10.0;
557	+
558	+	if (hasSlabBCenter)
559	+	slabBCenter_ = rnemdParams->getSlabBCenter();
560	+	else
561	+	slabBCenter_ = hmat(2,2) / 2.0;
562	+
563	+	selectionBstream << "select wrappedz > "
564	+	<< slabBCenter_ - 0.5*slabWidth_
565	+	<<  " && wrappedz < "
566	+	<< slabBCenter_ + 0.5*slabWidth_;
567	+	selectionB_ = selectionBstream.str();
568	+	} else {
569	+	if (hasSphereBRadius_) {
570	+	sphereBRadius_ = rnemdParams->getSphereBRadius();
571	+	selectionBstream << "select r > " << sphereBRadius_;
572	+	selectionB_ = selectionBstream.str();
573	+	} else {
574	+	selectionB_ = "select hull";
575	+	hasSelectionB_ = true;
576	+	}
577	+	}
578	+	}
579	+	}
580	+
581	+	// object evaluator:
582	+	evaluator_.loadScriptString(rnemdObjectSelection_);
583	+	seleMan_.setSelectionSet(evaluator_.evaluate());
584	+	evaluatorA_.loadScriptString(selectionA_);
585	+	evaluatorB_.loadScriptString(selectionB_);
586	+	seleManA_.setSelectionSet(evaluatorA_.evaluate());
587	+	seleManB_.setSelectionSet(evaluatorB_.evaluate());
588	+	commonA_ = seleManA_ & seleMan_;
589	+	commonB_ = seleManB_ & seleMan_;
590		}
591	<
409	<	RNEMD::~RNEMD() {
591	>
592
593	+	RNEMD::~RNEMD() {
594	+	if (!doRNEMD_) return;
595		#ifdef IS_MPI
596		if (worldRank == 0) {
597		#endif
#	Line 421 | Line 605 | namespace OpenMD {
605		#endif
606		}
607
608	<	bool RNEMD::inSlabA(Vector3d pos) {
609	<	return (abs(pos.z() - slabACenter_) < 0.5*slabWidth_);
610	<	}
611	<	bool RNEMD::inSlabB(Vector3d pos) {
428	<	return (abs(pos.z() - slabBCenter_) < 0.5*slabWidth_);
429	<	}
608	>	void RNEMD::doSwap(SelectionManager& smanA, SelectionManager& smanB) {
609	>	if (!doRNEMD_) return;
610	>	int selei;
611	>	int selej;
612
431	–	void RNEMD::doSwap() {
432	–
613		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
614		Mat3x3d hmat = currentSnap_->getHmat();
615
436	–	seleMan_.setSelectionSet(evaluator_.evaluate());
437	–
438	–	int selei;
616		StuntDouble* sd;
440	–	int idx;
617
618		RealType min_val;
619		bool min_found = false;
#	Line 447 | Line 623 | namespace OpenMD {
623		bool max_found = false;
624		StuntDouble* max_sd;
625
626	<	for (sd = seleMan_.beginSelected(selei); sd != NULL;
627	<	sd = seleMan_.nextSelected(selei)) {
626	>	for (sd = seleManA_.beginSelected(selei); sd != NULL;
627	>	sd = seleManA_.nextSelected(selei)) {
628
453	–	idx = sd->getLocalIndex();
454	–
629		Vector3d pos = sd->getPos();
630	<
630	>
631		// wrap the stuntdouble's position back into the box:
632	<
632	>
633		if (usePeriodicBoundaryConditions_)
634		currentSnap_->wrapVector(pos);
635	<	bool inA = inSlabA(pos);
636	<	bool inB = inSlabB(pos);
637	<
638	<	if (inA || inB) {
635	>
636	>	RealType mass = sd->getMass();
637	>	Vector3d vel = sd->getVel();
638	>	RealType value;
639	>
640	>	switch(rnemdFluxType_) {
641	>	case rnemdKE :
642
643	<	RealType mass = sd->getMass();
644	<	Vector3d vel = sd->getVel();
645	<	RealType value;
646	<
647	<	switch(rnemdFluxType_) {
471	<	case rnemdKE :
643	>	value = mass * vel.lengthSquare();
644	>
645	>	if (sd->isDirectional()) {
646	>	Vector3d angMom = sd->getJ();
647	>	Mat3x3d I = sd->getI();
648
649	<	value = mass * vel.lengthSquare();
650	<
651	<	if (sd->isDirectional()) {
652	<	Vector3d angMom = sd->getJ();
653	<	Mat3x3d I = sd->getI();
654	<
655	<	if (sd->isLinear()) {
656	<	int i = sd->linearAxis();
657	<	int j = (i + 1) % 3;
658	<	int k = (i + 2) % 3;
659	<	value += angMom[j] * angMom[j] / I(j, j) +
660	<	angMom[k] * angMom[k] / I(k, k);
661	<	} else {
662	<	value += angMom[0]*angMom[0]/I(0, 0)
663	<	+ angMom[1]*angMom[1]/I(1, 1)
664	<	+ angMom[2]*angMom[2]/I(2, 2);
665	<	}
666	<	} //angular momenta exchange enabled
667	<	//energyConvert temporarily disabled
668	<	//make kineticExchange_ comparable between swap & scale
669	<	//value = value * 0.5 / PhysicalConstants::energyConvert;
670	<	value *= 0.5;
671	<	break;
672	<	case rnemdPx :
673	<	value = mass * vel[0];
674	<	break;
675	<	case rnemdPy :
676	<	value = mass * vel[1];
677	<	break;
678	<	case rnemdPz :
679	<	value = mass * vel[2];
680	<	break;
681	<	default :
682	<	break;
649	>	if (sd->isLinear()) {
650	>	int i = sd->linearAxis();
651	>	int j = (i + 1) % 3;
652	>	int k = (i + 2) % 3;
653	>	value += angMom[j] * angMom[j] / I(j, j) +
654	>	angMom[k] * angMom[k] / I(k, k);
655	>	} else {
656	>	value += angMom[0]*angMom[0]/I(0, 0)
657	>	+ angMom[1]*angMom[1]/I(1, 1)
658	>	+ angMom[2]*angMom[2]/I(2, 2);
659	>	}
660	>	} //angular momenta exchange enabled
661	>	value *= 0.5;
662	>	break;
663	>	case rnemdPx :
664	>	value = mass * vel[0];
665	>	break;
666	>	case rnemdPy :
667	>	value = mass * vel[1];
668	>	break;
669	>	case rnemdPz :
670	>	value = mass * vel[2];
671	>	break;
672	>	default :
673	>	break;
674	>	}
675	>	if (!max_found) {
676	>	max_val = value;
677	>	max_sd = sd;
678	>	max_found = true;
679	>	} else {
680	>	if (max_val < value) {
681	>	max_val = value;
682	>	max_sd = sd;
683		}
684	+	}
685	+	}
686
687	<	if (inA == 0) {
688	<	if (!min_found) {
689	<	min_val = value;
690	<	min_sd = sd;
691	<	min_found = true;
692	<	} else {
693	<	if (min_val > value) {
694	<	min_val = value;
695	<	min_sd = sd;
696	<	}
697	<	}
698	<	} else {
699	<	if (!max_found) {
700	<	max_val = value;
701	<	max_sd = sd;
702	<	max_found = true;
703	<	} else {
704	<	if (max_val < value) {
705	<	max_val = value;
706	<	max_sd = sd;
707	<	}
708	<	}
709	<	}
687	>	for (sd = seleManB_.beginSelected(selej); sd != NULL;
688	>	sd = seleManB_.nextSelected(selej)) {
689	>
690	>	Vector3d pos = sd->getPos();
691	>
692	>	// wrap the stuntdouble's position back into the box:
693	>
694	>	if (usePeriodicBoundaryConditions_)
695	>	currentSnap_->wrapVector(pos);
696	>
697	>	RealType mass = sd->getMass();
698	>	Vector3d vel = sd->getVel();
699	>	RealType value;
700	>
701	>	switch(rnemdFluxType_) {
702	>	case rnemdKE :
703	>
704	>	value = mass * vel.lengthSquare();
705	>
706	>	if (sd->isDirectional()) {
707	>	Vector3d angMom = sd->getJ();
708	>	Mat3x3d I = sd->getI();
709	>
710	>	if (sd->isLinear()) {
711	>	int i = sd->linearAxis();
712	>	int j = (i + 1) % 3;
713	>	int k = (i + 2) % 3;
714	>	value += angMom[j] * angMom[j] / I(j, j) +
715	>	angMom[k] * angMom[k] / I(k, k);
716	>	} else {
717	>	value += angMom[0]*angMom[0]/I(0, 0)
718	>	+ angMom[1]*angMom[1]/I(1, 1)
719	>	+ angMom[2]*angMom[2]/I(2, 2);
720	>	}
721	>	} //angular momenta exchange enabled
722	>	value *= 0.5;
723	>	break;
724	>	case rnemdPx :
725	>	value = mass * vel[0];
726	>	break;
727	>	case rnemdPy :
728	>	value = mass * vel[1];
729	>	break;
730	>	case rnemdPz :
731	>	value = mass * vel[2];
732	>	break;
733	>	default :
734	>	break;
735		}
736	+
737	+	if (!min_found) {
738	+	min_val = value;
739	+	min_sd = sd;
740	+	min_found = true;
741	+	} else {
742	+	if (min_val > value) {
743	+	min_val = value;
744	+	min_sd = sd;
745	+	}
746	+	}
747		}
748
749	<	#ifdef IS_MPI
750	<	int nProc, worldRank;
749	>	#ifdef IS_MPI
750	>	int worldRank = MPI::COMM_WORLD.Get_rank();
751
538	–	nProc = MPI::COMM_WORLD.Get_size();
539	–	worldRank = MPI::COMM_WORLD.Get_rank();
540	–
752		bool my_min_found = min_found;
753		bool my_max_found = max_found;
754
#	Line 728 | Line 939 | namespace OpenMD {
939
940		switch(rnemdFluxType_) {
941		case rnemdKE:
731	–	cerr << "KE\n";
942		kineticExchange_ += max_val - min_val;
943		break;
944		case rnemdPx:
#	Line 741 | Line 951 | namespace OpenMD {
951		momentumExchange_.z() += max_val - min_val;
952		break;
953		default:
744	–	cerr << "default\n";
954		break;
955		}
956		} else {
#	Line 763 | Line 972 | namespace OpenMD {
972		}
973		}
974
975	<	void RNEMD::doNIVS() {
975	>	void RNEMD::doNIVS(SelectionManager& smanA, SelectionManager& smanB) {
976	>	if (!doRNEMD_) return;
977	>	int selei;
978	>	int selej;
979
980		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
981	+	RealType time = currentSnap_->getTime();
982		Mat3x3d hmat = currentSnap_->getHmat();
983
771	–	seleMan_.setSelectionSet(evaluator_.evaluate());
772	–
773	–	int selei;
984		StuntDouble* sd;
775	–	int idx;
985
986		vector<StuntDouble*> hotBin, coldBin;
987
#	Line 791 | Line 1000 | namespace OpenMD {
1000		RealType Kcz = 0.0;
1001		RealType Kcw = 0.0;
1002
1003	<	for (sd = seleMan_.beginSelected(selei); sd != NULL;
1004	<	sd = seleMan_.nextSelected(selei)) {
1003	>	for (sd = smanA.beginSelected(selei); sd != NULL;
1004	>	sd = smanA.nextSelected(selei)) {
1005
797	–	idx = sd->getLocalIndex();
798	–
1006		Vector3d pos = sd->getPos();
1007	<
1007	>
1008		// wrap the stuntdouble's position back into the box:
1009	<
1009	>
1010		if (usePeriodicBoundaryConditions_)
1011		currentSnap_->wrapVector(pos);
1012	<
1013	<	// which bin is this stuntdouble in?
1014	<	bool inA = inSlabA(pos);
1015	<	bool inB = inSlabB(pos);
1012	>
1013	>
1014	>	RealType mass = sd->getMass();
1015	>	Vector3d vel = sd->getVel();
1016	>
1017	>	hotBin.push_back(sd);
1018	>	Phx += mass * vel.x();
1019	>	Phy += mass * vel.y();
1020	>	Phz += mass * vel.z();
1021	>	Khx += mass * vel.x() * vel.x();
1022	>	Khy += mass * vel.y() * vel.y();
1023	>	Khz += mass * vel.z() * vel.z();
1024	>	if (sd->isDirectional()) {
1025	>	Vector3d angMom = sd->getJ();
1026	>	Mat3x3d I = sd->getI();
1027	>	if (sd->isLinear()) {
1028	>	int i = sd->linearAxis();
1029	>	int j = (i + 1) % 3;
1030	>	int k = (i + 2) % 3;
1031	>	Khw += angMom[j] * angMom[j] / I(j, j) +
1032	>	angMom[k] * angMom[k] / I(k, k);
1033	>	} else {
1034	>	Khw += angMom[0]*angMom[0]/I(0, 0)
1035	>	+ angMom[1]*angMom[1]/I(1, 1)
1036	>	+ angMom[2]*angMom[2]/I(2, 2);
1037	>	}
1038	>	}
1039	>	}
1040	>	for (sd = smanB.beginSelected(selej); sd != NULL;
1041	>	sd = smanB.nextSelected(selej)) {
1042	>	Vector3d pos = sd->getPos();
1043	>
1044	>	// wrap the stuntdouble's position back into the box:
1045	>
1046	>	if (usePeriodicBoundaryConditions_)
1047	>	currentSnap_->wrapVector(pos);
1048	>
1049	>	RealType mass = sd->getMass();
1050	>	Vector3d vel = sd->getVel();
1051
1052	<	if (inA || inB) {
1053	<
1054	<	RealType mass = sd->getMass();
1055	<	Vector3d vel = sd->getVel();
1056	<
1057	<	if (inA) {
1058	<	hotBin.push_back(sd);
1059	<	Phx += mass * vel.x();
1060	<	Phy += mass * vel.y();
1061	<	Phz += mass * vel.z();
1062	<	Khx += mass * vel.x() * vel.x();
1063	<	Khy += mass * vel.y() * vel.y();
1064	<	Khz += mass * vel.z() * vel.z();
1065	<	if (sd->isDirectional()) {
1066	<	Vector3d angMom = sd->getJ();
1067	<	Mat3x3d I = sd->getI();
1068	<	if (sd->isLinear()) {
1069	<	int i = sd->linearAxis();
1070	<	int j = (i + 1) % 3;
1071	<	int k = (i + 2) % 3;
1072	<	Khw += angMom[j] * angMom[j] / I(j, j) +
831	<	angMom[k] * angMom[k] / I(k, k);
832	<	} else {
833	<	Khw += angMom[0]*angMom[0]/I(0, 0)
834	<	+ angMom[1]*angMom[1]/I(1, 1)
835	<	+ angMom[2]*angMom[2]/I(2, 2);
836	<	}
837	<	}
838	<	} else {
839	<	coldBin.push_back(sd);
840	<	Pcx += mass * vel.x();
841	<	Pcy += mass * vel.y();
842	<	Pcz += mass * vel.z();
843	<	Kcx += mass * vel.x() * vel.x();
844	<	Kcy += mass * vel.y() * vel.y();
845	<	Kcz += mass * vel.z() * vel.z();
846	<	if (sd->isDirectional()) {
847	<	Vector3d angMom = sd->getJ();
848	<	Mat3x3d I = sd->getI();
849	<	if (sd->isLinear()) {
850	<	int i = sd->linearAxis();
851	<	int j = (i + 1) % 3;
852	<	int k = (i + 2) % 3;
853	<	Kcw += angMom[j] * angMom[j] / I(j, j) +
854	<	angMom[k] * angMom[k] / I(k, k);
855	<	} else {
856	<	Kcw += angMom[0]*angMom[0]/I(0, 0)
857	<	+ angMom[1]*angMom[1]/I(1, 1)
858	<	+ angMom[2]*angMom[2]/I(2, 2);
859	<	}
860	<	}
861	<	}
1052	>	coldBin.push_back(sd);
1053	>	Pcx += mass * vel.x();
1054	>	Pcy += mass * vel.y();
1055	>	Pcz += mass * vel.z();
1056	>	Kcx += mass * vel.x() * vel.x();
1057	>	Kcy += mass * vel.y() * vel.y();
1058	>	Kcz += mass * vel.z() * vel.z();
1059	>	if (sd->isDirectional()) {
1060	>	Vector3d angMom = sd->getJ();
1061	>	Mat3x3d I = sd->getI();
1062	>	if (sd->isLinear()) {
1063	>	int i = sd->linearAxis();
1064	>	int j = (i + 1) % 3;
1065	>	int k = (i + 2) % 3;
1066	>	Kcw += angMom[j] * angMom[j] / I(j, j) +
1067	>	angMom[k] * angMom[k] / I(k, k);
1068	>	} else {
1069	>	Kcw += angMom[0]*angMom[0]/I(0, 0)
1070	>	+ angMom[1]*angMom[1]/I(1, 1)
1071	>	+ angMom[2]*angMom[2]/I(2, 2);
1072	>	}
1073		}
1074		}
1075
#	Line 908 | Line 1119 | namespace OpenMD {
1119
1120		if ((c > 0.81) && (c < 1.21)) {//restrict scaling coefficients
1121		c = sqrt(c);
1122	<	//std::cerr << "cold slab scaling coefficient: " << c << endl;
912	<	//now convert to hotBin coefficient
1122	>
1123		RealType w = 0.0;
1124		if (rnemdFluxType_ ==  rnemdFullKE) {
1125		x = 1.0 + px * (1.0 - c);
#	Line 947 | Line 1157 | namespace OpenMD {
1157		}
1158		}
1159		w = sqrt(w);
950	–	// std::cerr << "xh= " << x << "\tyh= " << y << "\tzh= " << z
951	–	//           << "\twh= " << w << endl;
1160		for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
1161		if (rnemdFluxType_ == rnemdFullKE) {
1162		vel = (*sdi)->getVel();
#	Line 1211 | Line 1419 | namespace OpenMD {
1419		failTrialCount_++;
1420		}
1421		}
1422	<
1423	<	void RNEMD::doVSS() {
1422	>
1423	>	void RNEMD::doVSS(SelectionManager& smanA, SelectionManager& smanB) {
1424	>	if (!doRNEMD_) return;
1425	>	int selei;
1426	>	int selej;
1427
1428		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1429		RealType time = currentSnap_->getTime();
1430		Mat3x3d hmat = currentSnap_->getHmat();
1431
1221	–	seleMan_.setSelectionSet(evaluator_.evaluate());
1222	–
1223	–	int selei;
1432		StuntDouble* sd;
1225	–	int idx;
1433
1434		vector<StuntDouble*> hotBin, coldBin;
1435
1436		Vector3d Ph(V3Zero);
1437	+	Vector3d Lh(V3Zero);
1438		RealType Mh = 0.0;
1439	+	Mat3x3d Ih(0.0);
1440		RealType Kh = 0.0;
1441		Vector3d Pc(V3Zero);
1442	+	Vector3d Lc(V3Zero);
1443		RealType Mc = 0.0;
1444	+	Mat3x3d Ic(0.0);
1445		RealType Kc = 0.0;
1235	–
1446
1447	<	for (sd = seleMan_.beginSelected(selei); sd != NULL;
1448	<	sd = seleMan_.nextSelected(selei)) {
1447	>	// Constraints can be on only the linear or angular momentum, but
1448	>	// not both.  Usually, the user will specify which they want, but
1449	>	// in case they don't, the use of periodic boundaries should make
1450	>	// the choice for us.
1451	>	bool doLinearPart = false;
1452	>	bool doAngularPart = false;
1453
1454	<	idx = sd->getLocalIndex();
1454	>	switch (rnemdFluxType_) {
1455	>	case rnemdPx:
1456	>	case rnemdPy:
1457	>	case rnemdPz:
1458	>	case rnemdPvector:
1459	>	case rnemdKePx:
1460	>	case rnemdKePy:
1461	>	case rnemdKePvector:
1462	>	doLinearPart = true;
1463	>	break;
1464	>	case rnemdLx:
1465	>	case rnemdLy:
1466	>	case rnemdLz:
1467	>	case rnemdLvector:
1468	>	case rnemdKeLx:
1469	>	case rnemdKeLy:
1470	>	case rnemdKeLz:
1471	>	case rnemdKeLvector:
1472	>	doAngularPart = true;
1473	>	break;
1474	>	case rnemdKE:
1475	>	case rnemdRotKE:
1476	>	case rnemdFullKE:
1477	>	default:
1478	>	if (usePeriodicBoundaryConditions_)
1479	>	doLinearPart = true;
1480	>	else
1481	>	doAngularPart = true;
1482	>	break;
1483	>	}
1484	>
1485	>	for (sd = smanA.beginSelected(selei); sd != NULL;
1486	>	sd = smanA.nextSelected(selei)) {
1487
1488		Vector3d pos = sd->getPos();
1489
1490		// wrap the stuntdouble's position back into the box:
1491	+
1492	+	if (usePeriodicBoundaryConditions_)
1493	+	currentSnap_->wrapVector(pos);
1494	+
1495	+	RealType mass = sd->getMass();
1496	+	Vector3d vel = sd->getVel();
1497	+	Vector3d rPos = sd->getPos() - coordinateOrigin_;
1498	+	RealType r2;
1499	+
1500	+	hotBin.push_back(sd);
1501	+	Ph += mass * vel;
1502	+	Mh += mass;
1503	+	Kh += mass * vel.lengthSquare();
1504	+	Lh += mass * cross(rPos, vel);
1505	+	Ih -= outProduct(rPos, rPos) * mass;
1506	+	r2 = rPos.lengthSquare();
1507	+	Ih(0, 0) += mass * r2;
1508	+	Ih(1, 1) += mass * r2;
1509	+	Ih(2, 2) += mass * r2;
1510	+
1511	+	if (rnemdFluxType_ == rnemdFullKE) {
1512	+	if (sd->isDirectional()) {
1513	+	Vector3d angMom = sd->getJ();
1514	+	Mat3x3d I = sd->getI();
1515	+	if (sd->isLinear()) {
1516	+	int i = sd->linearAxis();
1517	+	int j = (i + 1) % 3;
1518	+	int k = (i + 2) % 3;
1519	+	Kh += angMom[j] * angMom[j] / I(j, j) +
1520	+	angMom[k] * angMom[k] / I(k, k);
1521	+	} else {
1522	+	Kh += angMom[0] * angMom[0] / I(0, 0) +
1523	+	angMom[1] * angMom[1] / I(1, 1) +
1524	+	angMom[2] * angMom[2] / I(2, 2);
1525	+	}
1526	+	}
1527	+	}
1528	+	}
1529	+	for (sd = smanB.beginSelected(selej); sd != NULL;
1530	+	sd = smanB.nextSelected(selej)) {
1531
1532	+	Vector3d pos = sd->getPos();
1533	+
1534	+	// wrap the stuntdouble's position back into the box:
1535	+
1536		if (usePeriodicBoundaryConditions_)
1537		currentSnap_->wrapVector(pos);
1538	+
1539	+	RealType mass = sd->getMass();
1540	+	Vector3d vel = sd->getVel();
1541	+	Vector3d rPos = sd->getPos() - coordinateOrigin_;
1542	+	RealType r2;
1543
1544	<	// which bin is this stuntdouble in?
1545	<	bool inA = inSlabA(pos);
1546	<	bool inB = inSlabB(pos);
1544	>	coldBin.push_back(sd);
1545	>	Pc += mass * vel;
1546	>	Mc += mass;
1547	>	Kc += mass * vel.lengthSquare();
1548	>	Lc += mass * cross(rPos, vel);
1549	>	Ic -= outProduct(rPos, rPos) * mass;
1550	>	r2 = rPos.lengthSquare();
1551	>	Ic(0, 0) += mass * r2;
1552	>	Ic(1, 1) += mass * r2;
1553	>	Ic(2, 2) += mass * r2;
1554
1555	<	if (inA || inB) {
1556	<
1557	<	RealType mass = sd->getMass();
1558	<	Vector3d vel = sd->getVel();
1559	<
1560	<	if (inA) {
1561	<	hotBin.push_back(sd);
1562	<	//std::cerr << "before, velocity = " << vel << endl;
1563	<	Ph += mass * vel;
1564	<	//std::cerr << "after, velocity = " << vel << endl;
1565	<	Mh += mass;
1566	<	Kh += mass * vel.lengthSquare();
1567	<	if (rnemdFluxType_ == rnemdFullKE) {
1568	<	if (sd->isDirectional()) {
1569	<	Vector3d angMom = sd->getJ();
1570	<	Mat3x3d I = sd->getI();
1269	<	if (sd->isLinear()) {
1270	<	int i = sd->linearAxis();
1271	<	int j = (i + 1) % 3;
1272	<	int k = (i + 2) % 3;
1273	<	Kh += angMom[j] * angMom[j] / I(j, j) +
1274	<	angMom[k] * angMom[k] / I(k, k);
1275	<	} else {
1276	<	Kh += angMom[0] * angMom[0] / I(0, 0) +
1277	<	angMom[1] * angMom[1] / I(1, 1) +
1278	<	angMom[2] * angMom[2] / I(2, 2);
1279	<	}
1280	<	}
1281	<	}
1282	<	} else { //midBin_
1283	<	coldBin.push_back(sd);
1284	<	Pc += mass * vel;
1285	<	Mc += mass;
1286	<	Kc += mass * vel.lengthSquare();
1287	<	if (rnemdFluxType_ == rnemdFullKE) {
1288	<	if (sd->isDirectional()) {
1289	<	Vector3d angMom = sd->getJ();
1290	<	Mat3x3d I = sd->getI();
1291	<	if (sd->isLinear()) {
1292	<	int i = sd->linearAxis();
1293	<	int j = (i + 1) % 3;
1294	<	int k = (i + 2) % 3;
1295	<	Kc += angMom[j] * angMom[j] / I(j, j) +
1296	<	angMom[k] * angMom[k] / I(k, k);
1297	<	} else {
1298	<	Kc += angMom[0] * angMom[0] / I(0, 0) +
1299	<	angMom[1] * angMom[1] / I(1, 1) +
1300	<	angMom[2] * angMom[2] / I(2, 2);
1301	<	}
1302	<	}
1303	<	}
1304	<	}
1555	>	if (rnemdFluxType_ == rnemdFullKE) {
1556	>	if (sd->isDirectional()) {
1557	>	Vector3d angMom = sd->getJ();
1558	>	Mat3x3d I = sd->getI();
1559	>	if (sd->isLinear()) {
1560	>	int i = sd->linearAxis();
1561	>	int j = (i + 1) % 3;
1562	>	int k = (i + 2) % 3;
1563	>	Kc += angMom[j] * angMom[j] / I(j, j) +
1564	>	angMom[k] * angMom[k] / I(k, k);
1565	>	} else {
1566	>	Kc += angMom[0] * angMom[0] / I(0, 0) +
1567	>	angMom[1] * angMom[1] / I(1, 1) +
1568	>	angMom[2] * angMom[2] / I(2, 2);
1569	>	}
1570	>	}
1571		}
1572		}
1573
1574		Kh *= 0.5;
1575		Kc *= 0.5;
1310	–
1311	–	// std::cerr << "Mh= " << Mh << "\tKh= " << Kh << "\tMc= " << Mc
1312	–	//        << "\tKc= " << Kc << endl;
1313	–	// std::cerr << "Ph= " << Ph << "\tPc= " << Pc << endl;
1576
1577		#ifdef IS_MPI
1578		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Ph[0], 3, MPI::REALTYPE, MPI::SUM);
1579		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Pc[0], 3, MPI::REALTYPE, MPI::SUM);
1580	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Lh[0], 3, MPI::REALTYPE, MPI::SUM);
1581	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Lc[0], 3, MPI::REALTYPE, MPI::SUM);
1582		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Mh, 1, MPI::REALTYPE, MPI::SUM);
1583		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kh, 1, MPI::REALTYPE, MPI::SUM);
1584		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Mc, 1, MPI::REALTYPE, MPI::SUM);
1585		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &Kc, 1, MPI::REALTYPE, MPI::SUM);
1586	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, Ih.getArrayPointer(), 9,
1587	+	MPI::REALTYPE, MPI::SUM);
1588	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, Ic.getArrayPointer(), 9,
1589	+	MPI::REALTYPE, MPI::SUM);
1590		#endif
1591	+
1592
1593	+	Vector3d ac, acrec, bc, bcrec;
1594	+	Vector3d ah, ahrec, bh, bhrec;
1595	+	RealType cNumerator, cDenominator;
1596	+	RealType hNumerator, hDenominator;
1597	+
1598	+
1599		bool successfulExchange = false;
1600		if ((Mh > 0.0) && (Mc > 0.0)) {//both slabs are not empty
1601		Vector3d vc = Pc / Mc;
1602	<	Vector3d ac = -momentumTarget_ / Mc + vc;
1603	<	Vector3d acrec = -momentumTarget_ / Mc;
1604	<	RealType cNumerator = Kc - kineticTarget_ - 0.5 * Mc * ac.lengthSquare();
1602	>	ac = -momentumTarget_ / Mc + vc;
1603	>	acrec = -momentumTarget_ / Mc;
1604	>
1605	>	// We now need the inverse of the inertia tensor to calculate the
1606	>	// angular velocity of the cold slab;
1607	>	Mat3x3d Ici = Ic.inverse();
1608	>	Vector3d omegac = Ici * Lc;
1609	>	bc  = -(Ici * angularMomentumTarget_) + omegac;
1610	>	bcrec = bc - omegac;
1611	>
1612	>	cNumerator = Kc - kineticTarget_;
1613	>	if (doLinearPart)
1614	>	cNumerator -= 0.5 * Mc * ac.lengthSquare();
1615	>
1616	>	if (doAngularPart)
1617	>	cNumerator -= 0.5 * ( dot(bc, Ic * bc));
1618	>
1619		if (cNumerator > 0.0) {
1620	<	RealType cDenominator = Kc - 0.5 * Mc * vc.lengthSquare();
1620	>
1621	>	cDenominator = Kc;
1622	>
1623	>	if (doLinearPart)
1624	>	cDenominator -= 0.5 * Mc * vc.lengthSquare();
1625	>
1626	>	if (doAngularPart)
1627	>	cDenominator -= 0.5*(dot(omegac, Ic * omegac));
1628	>
1629		if (cDenominator > 0.0) {
1630		RealType c = sqrt(cNumerator / cDenominator);
1631		if ((c > 0.9) && (c < 1.1)) {//restrict scaling coefficients
1632	+
1633		Vector3d vh = Ph / Mh;
1634	<	Vector3d ah = momentumTarget_ / Mh + vh;
1635	<	Vector3d ahrec = momentumTarget_ / Mh;
1636	<	RealType hNumerator = Kh + kineticTarget_
1637	<	- 0.5 * Mh * ah.lengthSquare();
1638	<	if (hNumerator > 0.0) {
1639	<	RealType hDenominator = Kh - 0.5 * Mh * vh.lengthSquare();
1634	>	ah = momentumTarget_ / Mh + vh;
1635	>	ahrec = momentumTarget_ / Mh;
1636	>
1637	>	// We now need the inverse of the inertia tensor to
1638	>	// calculate the angular velocity of the hot slab;
1639	>	Mat3x3d Ihi = Ih.inverse();
1640	>	Vector3d omegah = Ihi * Lh;
1641	>	bh  = (Ihi * angularMomentumTarget_) + omegah;
1642	>	bhrec = bh - omegah;
1643	>
1644	>	hNumerator = Kh + kineticTarget_;
1645	>	if (doLinearPart)
1646	>	hNumerator -= 0.5 * Mh * ah.lengthSquare();
1647	>
1648	>	if (doAngularPart)
1649	>	hNumerator -= 0.5 * ( dot(bh, Ih * bh));
1650	>
1651	>	if (hNumerator > 0.0) {
1652	>
1653	>	hDenominator = Kh;
1654	>	if (doLinearPart)
1655	>	hDenominator -= 0.5 * Mh * vh.lengthSquare();
1656	>	if (doAngularPart)
1657	>	hDenominator -= 0.5*(dot(omegah, Ih * omegah));
1658	>
1659		if (hDenominator > 0.0) {
1660		RealType h = sqrt(hNumerator / hDenominator);
1661		if ((h > 0.9) && (h < 1.1)) {
1662	<	// std::cerr << "cold slab scaling coefficient: " << c << "\n";
1346	<	// std::cerr << "hot slab scaling coefficient: " << h <<  "\n";
1662	>
1663		vector<StuntDouble*>::iterator sdi;
1664		Vector3d vel;
1665	+	Vector3d rPos;
1666	+
1667		for (sdi = coldBin.begin(); sdi != coldBin.end(); sdi++) {
1668		//vel = (*sdi)->getVel();
1669	<	vel = ((*sdi)->getVel() - vc) * c + ac;
1669	>	rPos = (*sdi)->getPos() - coordinateOrigin_;
1670	>	if (doLinearPart)
1671	>	vel = ((*sdi)->getVel() - vc) * c + ac;
1672	>	if (doAngularPart)
1673	>	vel = ((*sdi)->getVel() - cross(omegac, rPos)) * c + cross(bc, rPos);
1674	>
1675		(*sdi)->setVel(vel);
1676		if (rnemdFluxType_ == rnemdFullKE) {
1677		if ((*sdi)->isDirectional()) {
#	Line 1359 | Line 1682 | namespace OpenMD {
1682		}
1683		for (sdi = hotBin.begin(); sdi != hotBin.end(); sdi++) {
1684		//vel = (*sdi)->getVel();
1685	<	vel = ((*sdi)->getVel() - vh) * h + ah;
1685	>	rPos = (*sdi)->getPos() - coordinateOrigin_;
1686	>	if (doLinearPart)
1687	>	vel = ((*sdi)->getVel() - vh) * h + ah;
1688	>	if (doAngularPart)
1689	>	vel = ((*sdi)->getVel() - cross(omegah, rPos)) * h + cross(bh, rPos);
1690	>
1691		(*sdi)->setVel(vel);
1692		if (rnemdFluxType_ == rnemdFullKE) {
1693		if ((*sdi)->isDirectional()) {
#	Line 1371 | Line 1699 | namespace OpenMD {
1699		successfulExchange = true;
1700		kineticExchange_ += kineticTarget_;
1701		momentumExchange_ += momentumTarget_;
1702	+	angularMomentumExchange_ += angularMomentumTarget_;
1703		}
1704		}
1705		}
#	Line 1390 | Line 1719 | namespace OpenMD {
1719		}
1720		}
1721
1722	<	void RNEMD::doRNEMD() {
1722	>	RealType RNEMD::getDividingArea() {
1723
1724	+	if (hasDividingArea_) return dividingArea_;
1725	+
1726	+	RealType areaA, areaB;
1727	+	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
1728	+
1729	+	if (hasSelectionA_) {
1730	+	int isd;
1731	+	StuntDouble* sd;
1732	+	vector<StuntDouble*> aSites;
1733	+	seleManA_.setSelectionSet(evaluatorA_.evaluate());
1734	+	for (sd = seleManA_.beginSelected(isd); sd != NULL;
1735	+	sd = seleManA_.nextSelected(isd)) {
1736	+	aSites.push_back(sd);
1737	+	}
1738	+	ConvexHull* surfaceMeshA = new ConvexHull();
1739	+	surfaceMeshA->computeHull(aSites);
1740	+	areaA = surfaceMeshA->getArea();
1741	+	delete surfaceMeshA;
1742	+
1743	+	} else {
1744	+	if (usePeriodicBoundaryConditions_) {
1745	+	// in periodic boundaries, the surface area is twice the x-y
1746	+	// area of the current box:
1747	+	areaA = 2.0 * snap->getXYarea();
1748	+	} else {
1749	+	// in non-periodic simulations, without explicitly setting
1750	+	// selections, the sphere radius sets the surface area of the
1751	+	// dividing surface:
1752	+	areaA = 4.0 * M_PI * pow(sphereARadius_, 2);
1753	+	}
1754	+	}
1755	+
1756	+
1757	+
1758	+	if (hasSelectionB_) {
1759	+	int isd;
1760	+	StuntDouble* sd;
1761	+	vector<StuntDouble*> bSites;
1762	+	seleManB_.setSelectionSet(evaluatorB_.evaluate());
1763	+	for (sd = seleManB_.beginSelected(isd); sd != NULL;
1764	+	sd = seleManB_.nextSelected(isd)) {
1765	+	bSites.push_back(sd);
1766	+	}
1767	+	ConvexHull* surfaceMeshB = new ConvexHull();
1768	+	surfaceMeshB->computeHull(bSites);
1769	+	areaB = surfaceMeshB->getArea();
1770	+	delete surfaceMeshB;
1771	+
1772	+	} else {
1773	+	if (usePeriodicBoundaryConditions_) {
1774	+	// in periodic boundaries, the surface area is twice the x-y
1775	+	// area of the current box:
1776	+	areaB = 2.0 * snap->getXYarea();
1777	+	} else {
1778	+	// in non-periodic simulations, without explicitly setting
1779	+	// selections, but if a sphereBradius has been set, just use that:
1780	+	areaB = 4.0 * M_PI * pow(sphereBRadius_, 2);
1781	+	}
1782	+	}
1783	+
1784	+	dividingArea_ = min(areaA, areaB);
1785	+	hasDividingArea_ = true;
1786	+	return dividingArea_;
1787	+	}
1788	+
1789	+	void RNEMD::doRNEMD() {
1790	+	if (!doRNEMD_) return;
1791		trialCount_++;
1792	+
1793	+	// object evaluator:
1794	+	evaluator_.loadScriptString(rnemdObjectSelection_);
1795	+	seleMan_.setSelectionSet(evaluator_.evaluate());
1796	+
1797	+	evaluatorA_.loadScriptString(selectionA_);
1798	+	evaluatorB_.loadScriptString(selectionB_);
1799	+
1800	+	seleManA_.setSelectionSet(evaluatorA_.evaluate());
1801	+	seleManB_.setSelectionSet(evaluatorB_.evaluate());
1802	+
1803	+	commonA_ = seleManA_ & seleMan_;
1804	+	commonB_ = seleManB_ & seleMan_;
1805	+
1806	+	// Target exchange quantities (in each exchange) = dividingArea * dt * flux
1807	+	// dt = exchange time interval
1808	+	// flux = target flux
1809	+	// dividingArea = smallest dividing surface between the two regions
1810	+
1811	+	hasDividingArea_ = false;
1812	+	RealType area = getDividingArea();
1813	+
1814	+	kineticTarget_ = kineticFlux_ * exchangeTime_ * area;
1815	+	momentumTarget_ = momentumFluxVector_ * exchangeTime_ * area;
1816	+	angularMomentumTarget_ = angularMomentumFluxVector_ * exchangeTime_ * area;
1817	+
1818		switch(rnemdMethod_) {
1819		case rnemdSwap:
1820	<	doSwap();
1820	>	doSwap(commonA_, commonB_);
1821		break;
1822		case rnemdNIVS:
1823	<	doNIVS();
1823	>	doNIVS(commonA_, commonB_);
1824		break;
1825		case rnemdVSS:
1826	<	doVSS();
1826	>	doVSS(commonA_, commonB_);
1827		break;
1828		case rnemdUnkownMethod:
1829		default :
#	Line 1410 | Line 1832 | namespace OpenMD {
1832		}
1833
1834		void RNEMD::collectData() {
1835	<
1835	>	if (!doRNEMD_) return;
1836		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1837	+
1838	+	// collectData can be called more frequently than the doRNEMD, so use the
1839	+	// computed area from the last exchange time:
1840	+	RealType area = getDividingArea();
1841	+	areaAccumulator_->add(area);
1842		Mat3x3d hmat = currentSnap_->getHmat();
1416	–
1843		seleMan_.setSelectionSet(evaluator_.evaluate());
1844
1845	<	int selei;
1845	>	int selei(0);
1846		StuntDouble* sd;
1847	<	int idx;
1847	>	int binNo;
1848
1849		vector<RealType> binMass(nBins_, 0.0);
1850		vector<RealType> binPx(nBins_, 0.0);
1851		vector<RealType> binPy(nBins_, 0.0);
1852		vector<RealType> binPz(nBins_, 0.0);
1853	+	vector<RealType> binOmegax(nBins_, 0.0);
1854	+	vector<RealType> binOmegay(nBins_, 0.0);
1855	+	vector<RealType> binOmegaz(nBins_, 0.0);
1856		vector<RealType> binKE(nBins_, 0.0);
1857		vector<int> binDOF(nBins_, 0);
1858		vector<int> binCount(nBins_, 0);
#	Line 1431 | Line 1860 | namespace OpenMD {
1860		// alternative approach, track all molecules instead of only those
1861		// selected for scaling/swapping:
1862		/*
1863	<	SimInfo::MoleculeIterator miter;
1864	<	vector<StuntDouble*>::iterator iiter;
1865	<	Molecule* mol;
1866	<	StuntDouble* sd;
1867	<	for (mol = info_->beginMolecule(miter); mol != NULL;
1863	>	SimInfo::MoleculeIterator miter;
1864	>	vector<StuntDouble*>::iterator iiter;
1865	>	Molecule* mol;
1866	>	StuntDouble* sd;
1867	>	for (mol = info_->beginMolecule(miter); mol != NULL;
1868		mol = info_->nextMolecule(miter))
1869		sd is essentially sd
1870	<	for (sd = mol->beginIntegrableObject(iiter);
1871	<	sd != NULL;
1872	<	sd = mol->nextIntegrableObject(iiter))
1870	>	for (sd = mol->beginIntegrableObject(iiter);
1871	>	sd != NULL;
1872	>	sd = mol->nextIntegrableObject(iiter))
1873		*/
1874	+
1875		for (sd = seleMan_.beginSelected(selei); sd != NULL;
1876	<	sd = seleMan_.nextSelected(selei)) {
1877	<
1448	<	idx = sd->getLocalIndex();
1449	<
1876	>	sd = seleMan_.nextSelected(selei)) {
1877	>
1878		Vector3d pos = sd->getPos();
1879
1880		// wrap the stuntdouble's position back into the box:
1881
1882	<	if (usePeriodicBoundaryConditions_)
1882	>	if (usePeriodicBoundaryConditions_) {
1883		currentSnap_->wrapVector(pos);
1884	+	// which bin is this stuntdouble in?
1885	+	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
1886	+	// Shift molecules by half a box to have bins start at 0
1887	+	// The modulo operator is used to wrap the case when we are
1888	+	// beyond the end of the bins back to the beginning.
1889	+	binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
1890	+	} else {
1891	+	Vector3d rPos = pos - coordinateOrigin_;
1892	+	binNo = int(rPos.length() / binWidth_);
1893	+	}
1894
1457	–	// which bin is this stuntdouble in?
1458	–	// wrapped positions are in the range [-0.5*hmat(2,2), +0.5*hmat(2,2)]
1459	–	// Shift molecules by half a box to have bins start at 0
1460	–	// The modulo operator is used to wrap the case when we are
1461	–	// beyond the end of the bins back to the beginning.
1462	–	int binNo = int(nBins_ * (pos.z() / hmat(2,2) + 0.5)) % nBins_;
1463	–
1895		RealType mass = sd->getMass();
1896		Vector3d vel = sd->getVel();
1897	<
1898	<	binCount[binNo]++;
1899	<	binMass[binNo] += mass;
1900	<	binPx[binNo] += mass*vel.x();
1901	<	binPy[binNo] += mass*vel.y();
1902	<	binPz[binNo] += mass*vel.z();
1903	<	binKE[binNo] += 0.5 * (mass * vel.lengthSquare());
1904	<	binDOF[binNo] += 3;
1905	<
1906	<	if (sd->isDirectional()) {
1907	<	Vector3d angMom = sd->getJ();
1908	<	Mat3x3d I = sd->getI();
1909	<	if (sd->isLinear()) {
1910	<	int i = sd->linearAxis();
1911	<	int j = (i + 1) % 3;
1912	<	int k = (i + 2) % 3;
1913	<	binKE[binNo] += 0.5 * (angMom[j] * angMom[j] / I(j, j) +
1914	<	angMom[k] * angMom[k] / I(k, k));
1915	<	binDOF[binNo] += 2;
1916	<	} else {
1917	<	binKE[binNo] += 0.5 * (angMom[0] * angMom[0] / I(0, 0) +
1918	<	angMom[1] * angMom[1] / I(1, 1) +
1919	<	angMom[2] * angMom[2] / I(2, 2));
1920	<	binDOF[binNo] += 3;
1897	>	Vector3d rPos = sd->getPos() - coordinateOrigin_;
1898	>	Vector3d aVel = cross(rPos, vel);
1899	>
1900	>	if (binNo >= 0 && binNo < nBins_)  {
1901	>	binCount[binNo]++;
1902	>	binMass[binNo] += mass;
1903	>	binPx[binNo] += mass*vel.x();
1904	>	binPy[binNo] += mass*vel.y();
1905	>	binPz[binNo] += mass*vel.z();
1906	>	binOmegax[binNo] += aVel.x();
1907	>	binOmegay[binNo] += aVel.y();
1908	>	binOmegaz[binNo] += aVel.z();
1909	>	binKE[binNo] += 0.5 * (mass * vel.lengthSquare());
1910	>	binDOF[binNo] += 3;
1911	>
1912	>	if (sd->isDirectional()) {
1913	>	Vector3d angMom = sd->getJ();
1914	>	Mat3x3d I = sd->getI();
1915	>	if (sd->isLinear()) {
1916	>	int i = sd->linearAxis();
1917	>	int j = (i + 1) % 3;
1918	>	int k = (i + 2) % 3;
1919	>	binKE[binNo] += 0.5 * (angMom[j] * angMom[j] / I(j, j) +
1920	>	angMom[k] * angMom[k] / I(k, k));
1921	>	binDOF[binNo] += 2;
1922	>	} else {
1923	>	binKE[binNo] += 0.5 * (angMom[0] * angMom[0] / I(0, 0) +
1924	>	angMom[1] * angMom[1] / I(1, 1) +
1925	>	angMom[2] * angMom[2] / I(2, 2));
1926	>	binDOF[binNo] += 3;
1927	>	}
1928		}
1929		}
1930		}
1931
1494	–
1932		#ifdef IS_MPI
1933		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binCount[0],
1934		nBins_, MPI::INT, MPI::SUM);
#	Line 1503 | Line 1940 | namespace OpenMD {
1940		nBins_, MPI::REALTYPE, MPI::SUM);
1941		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binPz[0],
1942		nBins_, MPI::REALTYPE, MPI::SUM);
1943	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binOmegax[0],
1944	+	nBins_, MPI::REALTYPE, MPI::SUM);
1945	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binOmegay[0],
1946	+	nBins_, MPI::REALTYPE, MPI::SUM);
1947	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binOmegaz[0],
1948	+	nBins_, MPI::REALTYPE, MPI::SUM);
1949		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binKE[0],
1950		nBins_, MPI::REALTYPE, MPI::SUM);
1951		MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &binDOF[0],
#	Line 1510 | Line 1953 | namespace OpenMD {
1953		#endif
1954
1955		Vector3d vel;
1956	+	Vector3d aVel;
1957		RealType den;
1958		RealType temp;
1959		RealType z;
1960	+	RealType r;
1961		for (int i = 0; i < nBins_; i++) {
1962	<	z = (((RealType)i + 0.5) / (RealType)nBins_) * hmat(2,2);
1962	>	if (usePeriodicBoundaryConditions_) {
1963	>	z = (((RealType)i + 0.5) / (RealType)nBins_) * hmat(2,2);
1964	>	den = binMass[i] * nBins_ * PhysicalConstants::densityConvert
1965	>	/ currentSnap_->getVolume() ;
1966	>	} else {
1967	>	r = (((RealType)i + 0.5) * binWidth_);
1968	>	RealType rinner = (RealType)i * binWidth_;
1969	>	RealType router = (RealType)(i+1) * binWidth_;
1970	>	den = binMass[i] * 3.0 * PhysicalConstants::densityConvert
1971	>	/ (4.0 * M_PI * (pow(router,3) - pow(rinner,3)));
1972	>	}
1973		vel.x() = binPx[i] / binMass[i];
1974		vel.y() = binPy[i] / binMass[i];
1975		vel.z() = binPz[i] / binMass[i];
1976	<	den = binCount[i] * nBins_ / (hmat(0,0) * hmat(1,1) * hmat(2,2));
1977	<	temp = 2.0 * binKE[i] / (binDOF[i] * PhysicalConstants::kb *
1978	<	PhysicalConstants::energyConvert);
1976	>	aVel.x() = binOmegax[i] / binCount[i];
1977	>	aVel.y() = binOmegay[i] / binCount[i];
1978	>	aVel.z() = binOmegaz[i] / binCount[i];
1979
1980	<	for (unsigned int j = 0; j < outputMask_.size(); ++j) {
1981	<	if(outputMask_[j]) {
1982	<	switch(j) {
1983	<	case Z:
1984	<	(data_[j].accumulator[i])->add(z);
1985	<	break;
1986	<	case TEMPERATURE:
1987	<	data_[j].accumulator[i]->add(temp);
1988	<	break;
1989	<	case VELOCITY:
1990	<	dynamic_cast<VectorAccumulator *>(data_[j].accumulator[i])->add(vel);
1991	<	break;
1992	<	case DENSITY:
1993	<	data_[j].accumulator[i]->add(den);
1994	<	break;
1980	>	if (binCount[i] > 0) {
1981	>	// only add values if there are things to add
1982	>	temp = 2.0 * binKE[i] / (binDOF[i] * PhysicalConstants::kb *
1983	>	PhysicalConstants::energyConvert);
1984	>
1985	>	for (unsigned int j = 0; j < outputMask_.size(); ++j) {
1986	>	if(outputMask_[j]) {
1987	>	switch(j) {
1988	>	case Z:
1989	>	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(z);
1990	>	break;
1991	>	case R:
1992	>	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(r);
1993	>	break;
1994	>	case TEMPERATURE:
1995	>	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(temp);
1996	>	break;
1997	>	case VELOCITY:
1998	>	dynamic_cast<VectorAccumulator *>(data_[j].accumulator[i])->add(vel);
1999	>	break;
2000	>	case ANGULARVELOCITY:
2001	>	dynamic_cast<VectorAccumulator *>(data_[j].accumulator[i])->add(aVel);
2002	>	break;
2003	>	case DENSITY:
2004	>	dynamic_cast<Accumulator *>(data_[j].accumulator[i])->add(den);
2005	>	break;
2006	>	}
2007		}
2008		}
2009		}
#	Line 1544 | Line 2011 | namespace OpenMD {
2011		}
2012
2013		void RNEMD::getStarted() {
2014	+	if (!doRNEMD_) return;
2015	+	hasDividingArea_ = false;
2016		collectData();
2017		writeOutputFile();
2018		}
2019
2020		void RNEMD::parseOutputFileFormat(const std::string& format) {
2021	+	if (!doRNEMD_) return;
2022		StringTokenizer tokenizer(format, " ,;|\t\n\r");
2023
2024		while(tokenizer.hasMoreTokens()) {
#	Line 1569 | Line 2039 | namespace OpenMD {
2039		}
2040
2041		void RNEMD::writeOutputFile() {
2042	+	if (!doRNEMD_) return;
2043
2044		#ifdef IS_MPI
2045		// If we're the root node, should we print out the results
#	Line 1588 | Line 2059 | namespace OpenMD {
2059		Snapshot* currentSnap_ = info_->getSnapshotManager()->getCurrentSnapshot();
2060
2061		RealType time = currentSnap_->getTime();
2062	<
2063	<
2062	>	RealType avgArea;
2063	>	areaAccumulator_->getAverage(avgArea);
2064	>	RealType Jz = kineticExchange_ / (time * avgArea)
2065	>	/ PhysicalConstants::energyConvert;
2066	>	Vector3d JzP = momentumExchange_ / (time * avgArea);
2067	>	Vector3d JzL = angularMomentumExchange_ / (time * avgArea);
2068	>
2069		rnemdFile_ << "#######################################################\n";
2070		rnemdFile_ << "# RNEMD {\n";
2071
2072		map<string, RNEMDMethod>::iterator mi;
2073		for(mi = stringToMethod_.begin(); mi != stringToMethod_.end(); ++mi) {
2074		if ( (*mi).second == rnemdMethod_)
2075	<	rnemdFile_ << "#    exchangeMethod  = " << (*mi).first << "\n";
2075	>	rnemdFile_ << "#    exchangeMethod  = \"" << (*mi).first << "\";\n";
2076		}
2077		map<string, RNEMDFluxType>::iterator fi;
2078		for(fi = stringToFluxType_.begin(); fi != stringToFluxType_.end(); ++fi) {
2079		if ( (*fi).second == rnemdFluxType_)
2080	<	rnemdFile_ << "#    fluxType  = " << (*fi).first << "\n";
2080	>	rnemdFile_ << "#    fluxType  = \"" << (*fi).first << "\";\n";
2081		}
2082
2083	<	rnemdFile_ << "#    exchangeTime = " << exchangeTime_ << " fs\n";
2083	>	rnemdFile_ << "#    exchangeTime = " << exchangeTime_ << ";\n";
2084
2085		rnemdFile_ << "#    objectSelection = \""
2086	<	<< rnemdObjectSelection_ << "\"\n";
2087	<	rnemdFile_ << "#    slabWidth = " << slabWidth_ << " angstroms\n";
2088	<	rnemdFile_ << "#    slabAcenter = " << slabACenter_ << " angstroms\n";
1613	<	rnemdFile_ << "#    slabBcenter = " << slabBCenter_ << " angstroms\n";
2086	>	<< rnemdObjectSelection_ << "\";\n";
2087	>	rnemdFile_ << "#    selectionA = \"" << selectionA_ << "\";\n";
2088	>	rnemdFile_ << "#    selectionB = \"" << selectionB_ << "\";\n";
2089		rnemdFile_ << "# }\n";
2090		rnemdFile_ << "#######################################################\n";
2091	<
2092	<	rnemdFile_ << "# running time = " << time << " fs\n";
2093	<	rnemdFile_ << "# target kinetic flux = " << kineticFlux_ << "\n";
2094	<	rnemdFile_ << "# target momentum flux = " << momentumFluxVector_ << "\n";
2095	<
2096	<	rnemdFile_ << "# target one-time kinetic exchange = " << kineticTarget_
2097	<	<< "\n";
2098	<	rnemdFile_ << "# target one-time momentum exchange = " << momentumTarget_
2099	<	<< "\n";
2100	<
2101	<	rnemdFile_ << "# actual kinetic exchange = " << kineticExchange_ << "\n";
2102	<	rnemdFile_ << "# actual momentum exchange = " << momentumExchange_
2103	<	<< "\n";
2104	<
2105	<	rnemdFile_ << "# attempted exchanges: " << trialCount_ << "\n";
2106	<	rnemdFile_ << "# failed exchanges: " << failTrialCount_ << "\n";
2107	<
2108	<
2091	>	rnemdFile_ << "# RNEMD report:\n";
2092	>	rnemdFile_ << "#      running time = " << time << " fs\n";
2093	>	rnemdFile_ << "# Target flux:\n";
2094	>	rnemdFile_ << "#           kinetic = "
2095	>	<< kineticFlux_ / PhysicalConstants::energyConvert
2096	>	<< " (kcal/mol/A^2/fs)\n";
2097	>	rnemdFile_ << "#          momentum = " << momentumFluxVector_
2098	>	<< " (amu/A/fs^2)\n";
2099	>	rnemdFile_ << "#  angular momentum = " << angularMomentumFluxVector_
2100	>	<< " (amu/A^2/fs^2)\n";
2101	>	rnemdFile_ << "# Target one-time exchanges:\n";
2102	>	rnemdFile_ << "#          kinetic = "
2103	>	<< kineticTarget_ / PhysicalConstants::energyConvert
2104	>	<< " (kcal/mol)\n";
2105	>	rnemdFile_ << "#          momentum = " << momentumTarget_
2106	>	<< " (amu*A/fs)\n";
2107	>	rnemdFile_ << "#  angular momentum = " << angularMomentumTarget_
2108	>	<< " (amu*A^2/fs)\n";
2109	>	rnemdFile_ << "# Actual exchange totals:\n";
2110	>	rnemdFile_ << "#          kinetic = "
2111	>	<< kineticExchange_ / PhysicalConstants::energyConvert
2112	>	<< " (kcal/mol)\n";
2113	>	rnemdFile_ << "#          momentum = " << momentumExchange_
2114	>	<< " (amu*A/fs)\n";
2115	>	rnemdFile_ << "#  angular momentum = " << angularMomentumExchange_
2116	>	<< " (amu*A^2/fs)\n";
2117	>	rnemdFile_ << "# Actual flux:\n";
2118	>	rnemdFile_ << "#          kinetic = " << Jz
2119	>	<< " (kcal/mol/A^2/fs)\n";
2120	>	rnemdFile_ << "#          momentum = " << JzP
2121	>	<< " (amu/A/fs^2)\n";
2122	>	rnemdFile_ << "#  angular momentum = " << JzL
2123	>	<< " (amu/A^2/fs^2)\n";
2124	>	rnemdFile_ << "# Exchange statistics:\n";
2125	>	rnemdFile_ << "#               attempted = " << trialCount_ << "\n";
2126	>	rnemdFile_ << "#                  failed = " << failTrialCount_ << "\n";
2127		if (rnemdMethod_ == rnemdNIVS) {
2128	<	rnemdFile_ << "# NIVS root-check warnings: " << failRootCount_ << "\n";
2128	>	rnemdFile_ << "#  NIVS root-check errors = "
2129	>	<< failRootCount_ << "\n";
2130		}
1637	–
2131		rnemdFile_ << "#######################################################\n";
2132
2133
#	Line 1645 | Line 2138 | namespace OpenMD {
2138		if (outputMask_[i]) {
2139		rnemdFile_ << "\t" << data_[i].title <<
2140		"(" << data_[i].units << ")";
2141	+	// add some extra tabs for column alignment
2142	+	if (data_[i].dataType == "Vector3d") rnemdFile_ << "\t\t";
2143		}
2144		}
2145		rnemdFile_ << std::endl;
2146
2147		rnemdFile_.precision(8);
2148
2149	<	for (unsigned int j = 0; j < nBins_; j++) {
2149	>	for (int j = 0; j < nBins_; j++) {
2150
2151		for (unsigned int i = 0; i < outputMask_.size(); ++i) {
2152		if (outputMask_[i]) {
2153		if (data_[i].dataType == "RealType")
2154		writeReal(i,j);
2155	<	else if (data_[i].dataType == "Vector3d")
2155	>	else if (data_[i].dataType == "Vector3d")
2156		writeVector(i,j);
2157		else {
2158		sprintf( painCave.errMsg,
#	Line 1671 | Line 2166 | namespace OpenMD {
2166		rnemdFile_ << std::endl;
2167
2168		}
2169	+
2170	+	rnemdFile_ << "#######################################################\n";
2171	+	rnemdFile_ << "# Standard Deviations in those quantities follow:\n";
2172	+	rnemdFile_ << "#######################################################\n";
2173	+
2174	+
2175	+	for (int j = 0; j < nBins_; j++) {
2176	+	rnemdFile_ << "#";
2177	+	for (unsigned int i = 0; i < outputMask_.size(); ++i) {
2178	+	if (outputMask_[i]) {
2179	+	if (data_[i].dataType == "RealType")
2180	+	writeRealStdDev(i,j);
2181	+	else if (data_[i].dataType == "Vector3d")
2182	+	writeVectorStdDev(i,j);
2183	+	else {
2184	+	sprintf( painCave.errMsg,
2185	+	"RNEMD found an unknown data type for: %s ",
2186	+	data_[i].title.c_str());
2187	+	painCave.isFatal = 1;
2188	+	simError();
2189	+	}
2190	+	}
2191	+	}
2192	+	rnemdFile_ << std::endl;
2193	+
2194	+	}
2195
2196		rnemdFile_.flush();
2197		rnemdFile_.close();
#	Line 1682 | Line 2203 | namespace OpenMD {
2203		}
2204
2205		void RNEMD::writeReal(int index, unsigned int bin) {
2206	+	if (!doRNEMD_) return;
2207		assert(index >=0 && index < ENDINDEX);
2208	<	assert(bin >=0 && bin < nBins_);
2208	>	assert(int(bin) < nBins_);
2209		RealType s;
2210	+	int count;
2211
2212	<	data_[index].accumulator[bin]->getAverage(s);
2212	>	count = data_[index].accumulator[bin]->count();
2213	>	if (count == 0) return;
2214
2215	+	dynamic_cast<Accumulator *>(data_[index].accumulator[bin])->getAverage(s);
2216	+
2217		if (! isinf(s) && ! isnan(s)) {
2218		rnemdFile_ << "\t" << s;
2219		} else{
#	Line 1700 | Line 2226 | namespace OpenMD {
2226		}
2227
2228		void RNEMD::writeVector(int index, unsigned int bin) {
2229	+	if (!doRNEMD_) return;
2230		assert(index >=0 && index < ENDINDEX);
2231	<	assert(bin >=0 && bin < nBins_);
2231	>	assert(int(bin) < nBins_);
2232		Vector3d s;
2233	+	int count;
2234	+
2235	+	count = data_[index].accumulator[bin]->count();
2236	+
2237	+	if (count == 0) return;
2238	+
2239		dynamic_cast<VectorAccumulator*>(data_[index].accumulator[bin])->getAverage(s);
2240		if (isinf(s[0]) || isnan(s[0]) ||
2241		isinf(s[1]) || isnan(s[1]) ||
#	Line 1716 | Line 2249 | namespace OpenMD {
2249		rnemdFile_ << "\t" << s[0] << "\t" << s[1] << "\t" << s[2];
2250		}
2251		}
2252	+
2253	+	void RNEMD::writeRealStdDev(int index, unsigned int bin) {
2254	+	if (!doRNEMD_) return;
2255	+	assert(index >=0 && index < ENDINDEX);
2256	+	assert(int(bin) < nBins_);
2257	+	RealType s;
2258	+	int count;
2259	+
2260	+	count = data_[index].accumulator[bin]->count();
2261	+	if (count == 0) return;
2262	+
2263	+	dynamic_cast<Accumulator *>(data_[index].accumulator[bin])->getStdDev(s);
2264	+
2265	+	if (! isinf(s) && ! isnan(s)) {
2266	+	rnemdFile_ << "\t" << s;
2267	+	} else{
2268	+	sprintf( painCave.errMsg,
2269	+	"RNEMD detected a numerical error writing: %s std. dev. for bin %d",
2270	+	data_[index].title.c_str(), bin);
2271	+	painCave.isFatal = 1;
2272	+	simError();
2273	+	}
2274	+	}
2275	+
2276	+	void RNEMD::writeVectorStdDev(int index, unsigned int bin) {
2277	+	if (!doRNEMD_) return;
2278	+	assert(index >=0 && index < ENDINDEX);
2279	+	assert(int(bin) < nBins_);
2280	+	Vector3d s;
2281	+	int count;
2282	+
2283	+	count = data_[index].accumulator[bin]->count();
2284	+	if (count == 0) return;
2285	+
2286	+	dynamic_cast<VectorAccumulator*>(data_[index].accumulator[bin])->getStdDev(s);
2287	+	if (isinf(s[0]) || isnan(s[0]) ||
2288	+	isinf(s[1]) || isnan(s[1]) ||
2289	+	isinf(s[2]) || isnan(s[2]) ) {
2290	+	sprintf( painCave.errMsg,
2291	+	"RNEMD detected a numerical error writing: %s std. dev. for bin %d",
2292	+	data_[index].title.c_str(), bin);
2293	+	painCave.isFatal = 1;
2294	+	simError();
2295	+	} else {
2296	+	rnemdFile_ << "\t" << s[0] << "\t" << s[1] << "\t" << s[2];
2297	+	}
2298	+	}
2299		}
2300

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